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        Ko and Qun Ma and Matthew Nyerges and Troy Raeder and Thomas Slabach
        and Jes\'{u}s A. Izaguirre},
  title = {\textsc{{P}roto{M}ol}: {A}n Object-Oriented Framework for Prototyping
        Novel Algorithms for Molecular Dynamics},
  journal = ACMTMS,
  year = {2004},
  volume = {30},
  pages = {237--265},
  number = {3}
}

@INPROCEEDINGS{MaIz01,
  author = {T. Matthey and J.~A. Izaguirre},
  title = {Proto{M}ol: A Molecular Dynamics Framework with Incremental Parallelization},
  booktitle = {Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific
        Computing (PP01)},
  year = {2001},
  series = {Proceedings in Applied Mathematics},
  address = {Philadelphia},
  month = MAR,
  publisher = {Society for Industrial and Applied Mathematics},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/proto.pdf}}
}

@ARTICLE{EGCS03,
  author = {R.~Elber and A.~Ghosh and A.~Cardenas and H.~Stern},
  title = {Bridging the gap between reaction pathways, long time dynamics and
        calculation of rates},
  journal = ACP,
  year = {2003},
  volume = {126},
  pages = {93-129}
}

@Article{ElGC02,
  author = {R.~Elber and A.~Ghosh and A.~Cardenas},
  title = {Long Time Dynamics of Complex Systems},
  journal = ACR,
  year = {2002},
  volume = 35,
  pages = {396-403}
}

@ARTICLE{FarE04,
  author = {A.~K.~Faradjian and R.~Elber},
  title = {Computing time scales from reaction coordinates by milestoning},
  journal = JCP,
  year = {2004},
  volume = {120},
  pages = {10880-10889},
  number = {23}
}

@Article{Cick09,
  author = {Trevor Cickovski and Santanu Chatterjee and Jacob Wenger and Chris Sweet and Jes\'{u}s A. Izaguirre},
  title = {MDLab : A Molecular Dynamics Simulation Prototyping Environment},
  journal = JCC,
  year = {2009},
  volume = {30},
  pages = {1000}
}

@BOOK{Schl02,
  title = {Molecular Modeling and Simulation - An Interdisciplinary Guide},
  publisher = {Springer-Verlag},
  year = {2002},
  author = {Tamar Schlick},
  address = {New York, NY},
  remark = {ISBN: 0-387-95404-X}
}

@Article{ZhCY09,
  author = {L.~Zheng and M.~Chen and W.~Yang},
  title = {Simultaneous escaping of explicit and hidden free energy barriers : Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling},
  journal = JCP,
  year = {2009},
  volume = {130},
  number = {10},
  pages = {234105},
}

@Article{BrHC09,
  author = {Jason B.~Brokaw and Kevin R.~Haas and Jhih-Wei Chu},
  title = {Reaction path optimization with Holonomic constraints and kinetic energy potential},
  journal = JCTC,
  year = 2009,
  volume = {5},
  pages = {2050-2061}
}

@ARTICLE{BaSc98b,
  author = {Eric Barth and Tamar Schlick},
  title = {Extrapolation Versus Impulse in Multiple-Timestepping Schemes. {II}.
        {L}inear Analysis and Applications to {N}ewtonian and {L}angevin
        Dynamics},
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  year = {1998},
  volume = {109},
  pages = {1633--1642},
  number = {5}
}

@ARTICLE{FLZB97,
  author = {Fransisco Figueirido and Ronald M. Levy and Ruhong Zhou and Bruce
        J. Berne},
  title = {Large Scale Simulation of Macromolecules in Solution: Combining the
        Periodic Fast Multipole Method with Multiple Time Step Integrators},
  journal = {J. Chem.\ Phys.},
  year = {1997},
  volume = {106},
  pages = {9835--9849},
  number = {23}
}

@ARTICLE{WaKa95,
  author = {Masakatsu Watanabe and Martin Karplus},
  title = {Simulation of Macromolecules by Multiple-Time-Step Methods},
  journal = {J. Phys.\ Chem.},
  year = {1995},
  volume = {99},
  pages = {5680--5697},
  number = {15},
  nabstract = {Molecular dynamics simulations of macromolecules require long computation
        times to generate the trajectories needed for determining their thermodynamic
        and dynamic properties. The most rapidly varying quantities, such
        as the bond lengths, limit the integration time step, while the more
        slowly varying molecular processes are of primary interest. The form
        of the empirical potential energy function used in simulations of
        macromolecules makes it possible to exploit the existing separation
        of time scales by use of the reversible multiple time-step method
        (Tuckerman, Berne, and Martyna. J. Chem. Phys. 1992, 97, 1990). Implementation
        of the method in Cartesian coordinates yields an efficient multiple
        time-step algorithm for molecular dynamics with a velocity Verlet
        integrator. The forces acting on individual atoms are classified
        as hard, medium, and soft; for example, hard forces are contributed
        by bond-stretching and bond-angle bending terms, medium forces by
        dihedral angle and nonbonded (van der Waals and electrostatic) interaction
        terms acting on hydrogen atoms, and soft forces by the remaining
        nonbonded interaction terms. The multiple time-step approach is tested
        in short (10 ps) simulations of the pentapeptide Met-enkephalin and
        the protein the bovine pancreatic trypsin inhibitor. The stability
        of the integration methods and the dynamics and structural results
        are compared with those obtained with standard single time-step methods,
        with and without SHAKE. The results demonstrate that, for peptides
        and proteins, the multiple time-step method yields stable trajectories
        with a saving of up to a factors of 4 in computer time. Some properties
        (e.g., relaxation times, hydrogen bonding characteristics) are given
        accurately in short simulations (10 ps) even from unstable integrators
        with large time steps. A series of longer simulations (100 ps) of
        BPTI confirm many of the results found in the shorter simulations.
        However, some larger differences in behavior result from the use
        of less stable integration algorithms; in one case, the simulation
        diverges. Also, use of the SHAKE algorithm for a hydrogen atoms containing
        bonds with a stable integrator is shown to affect some properties
        of the system (e.g., the spectral densities associated with the main
        chain and side chain torsional motions). The sensitivity appears
        to arise from the large number of hydrogen atoms in proteins and
        from the densely packed nature of the structures. Thus, a detailed
        treatment of the hydrogen atoms, including their bond length fluctuations,
        appears to be important for obtaining highly accurate dynamics of
        proteins.}
}

@ARTICLE{MaIz03a,
  author = {Q.\ Ma and J.~A.\ Izaguirre},
  title = {Targeted Mollified Impulse --- a Multiscale Stochastic Integrator
        for Long Molecular Dynamics Simulations},
  journal = MMS,
  year = {2003},
  volume = {2},
  pages = {1--21},
  number = {1}
}

@ARTICLE{CRYB05,
  author = {C.~Chennubhotla and A.~J.~Rader and L.~Yang and I.~Bahar},
  title = {Elastic Network models for understanding biomolecular machinery:from
        enzymes to supramolecular assemblies},
  journal = PHCB,
  year = {2005},
  volume = {2},
  pages = {S173-S180}
}

@ARTICLE{ZhSS10,
  author = {R.~Zhao and J.~Shen and R.~D.~Skeel},
  title = {Maximum flux transition paths of conformational change},
  journal = JCTC,
  year = {2010},
  volume = {6},
  pages = {2411-2423}
}


@ARTICLE{HaKG95,
  author = {S.~Hayward and A.~Kitao and N.~G{\=o}},
  title = {Harmonicity and anharmonicity in protein dynamics: A normal
mode analysis and principal component analysis},
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  year = {1995},
  volume = {23},
  pages = {177-186},
  number = {2}
}

@ARTICLE{KiSG98,
  author = {A.~Kitao and S.~Hayward and N.~G{\=o}},
  title = {Energy landscape of a native protein: Jumping among minima model},
  journal = PSFB,
  year = {1998},
  volume = {33},
  pages = {496-517},
  number = {4}
}


@ARTICLE{SeBB10,
  author = {R.~S.~Sedeh and M.~Bathe and K.~J.~Bathe},
  title = {The subspace iteration method in protein normal mode analysis},
  journal = JCC,
  year = {2010},
  volume = {31},
  pages = {66-74},
  number = {1}
}

@ARTICLE{Ghys10,
  author = {A.~Ghysels and V.~ Van Speybroeck and E.~Pauwels
and S.~Catak and B.~R.~Brooks and D.~Van Neck and
 M.~Waroquier},
  title = {Comparative study of various normal mode analysis techniques
based on partial {H}essians},
  journal = JCC,
  year = {2010},
  volume = {31},
  pages = {994-1007},
  number = {4}
}
@ARTICLE{MouP93,
  author = {L.~Mouawad and D.~Perahia},
  title = {Diagonalization in a mixed basis: A method to compute
low-frequency normal modes for large macromolecules},
  journal = BP,
  year = {1993},
  volume = {33},
  pages = {599-611},
  number = {4}
}

@Article{DuTS94,
 author =  {P.~Durand and G.~Trinquier and Y.~H.~Sanejouand},
 title =  {A new approach for determining low-frequency normal modes
in macromolecules},
 journal =  BP,
 year =  {1994},
 volume =  {34},
 pages =  {759-771}
}

@Article{OnCB02,
 author = {A.~Onufriev and D.~A.~Case and A.~Bashford},
 title = {Effective {B}orn radii in the {G}eneralized {B}orn
approximation: The importance of being perfect},
 journal = JCC,
 year = 2002,
 volume = 23,
 number = 14,
 pages = {1297-1304}
}

@article{Ortoleva:2008p1554,
author = {P Ortoleva}, 
journal = JSP,
title = {Curvilinear all-atom multiscale ({CAM}) theory of macromolecular dynamics},
abstract = {Abstract A method is introduced for simulating long timescale macromolecular structural fluctuations and transitions with atomic-scale detail. The N-atom Liouville equation for the macromolecule/host medium system provides the starting point for the analysis. Order pa- ...},
year = {2008},
month = {Jan},
date-added = {2011-08-30 10:46:36 -0400},
date-modified = {2011-08-30 10:46:36 -0400},
pmid = {10413776166837491907related:wxjHyj8qhZAJ},
uri = {papers://7AF1B0BF-417E-4A82-A1A8-0E97759761F6/Paper/p1554},
rating = {0}
}


%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Altis:2007p1500,
author = {A Altis and P Nguyen and G Stock}, 
journal = PRL,
title = {How complex is the dynamics of peptide folding?},
abstract = {Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with ...},
year = {2007},
month = {Jan},
date-added = {2011-08-30 10:24:30 -0400},
date-modified = {2011-08-30 10:24:30 -0400},
pmid = {15872772487195554585related:GXPiw3pqR9wJ},
rating = {0}
}

@article{Nguyen:2007p1501,
author = {P Nguyen and R Hegger and G Stock}, 
journal = JCP,
title = {Dihedral angle principal component analysis of molecular dynamics simulations},
abstract = {It has recently been suggested by Mu et al. [Proteins [bold 58], 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates ...},
year = {2007},
month = {Jan},
date-added = {2011-08-30 10:24:30 -0400},
date-modified = {2011-08-30 10:24:30 -0400},
pmid = {1022371532299617480related:yMQw630xMA4J},
rating = {0}
}

@article{Nguyen:2008p1502,
author = {P Nguyen and R Hegger and G Stock}, 
journal = JCP,
title = {Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis},
abstract = {A systematic approach to construct a low-dimensional free energy landscape from a classical molecular dynamics (MD) simulation is presented. The approach is based on the recently proposed dihedral angle principal component analysis (dPCA), which avoids artifacts due to the ...},
year = {2008},
month = {Jan},
date-added = {2011-08-30 10:24:30 -0400},
date-modified = {2011-08-30 10:24:30 -0400},
pmid = {15920830421529783725related:re2DjOom8twJ},
rating = {0}
}



%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Hu:2008p1447,
author = {J Hu and A Ma and A R Dinner}, 
journal = PNAS,
title = {A two-step nucleotide-flipping mechanism enables kinetic discrimination of {DNA} lesions by {AGT}},
abstract = {... Ma A ,; Dinner AR. (2005) Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B 109:6769--6779. Medline. ↵.},
year = {2008},
month = {Jan},
date-added = {2011-08-29 20:46:20 -0400},
date-modified = {2011-08-29 20:46:20 -0400},
pmid = {2408966963801925689related:OagQubBebiEJ},
read = {Yes},
rating = {0}
}

@article{Qi:2010p1445,
author = {B Qi and S Muff and A Caflisch and A R Dinner}, 
journal = JPCB,
title = {Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a $\beta$-Sheet Miniprotein},
number = {20},
pages = {6979--6989},
volume = {114},
year = {2010},
date-added = {2011-08-29 20:37:05 -0400},
date-modified = {2011-08-29 20:38:22 -0400},
pmid = {10068942009870876633related:2X9cEmkRvIsJ},
local-url = {file://localhost/Users/izaguirr/Documents/Papers/2010/Qi/Qi_2010_The%20Journal%20of%20Physical%20Chemistry%20B.pdf},
uri = {papers://7AF1B0BF-417E-4A82-A1A8-0E97759761F6/Paper/p1445},
read = {Yes},
rating = {0}
}



%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Ma:2005p1444,
author = {A Ma and R Aaron}, 
journal = JPCB,
title = {Automatic method for identifying reaction coordinates in complex systems},
number = {14},
pages = {6769--6779},
volume = {109},
year = {2005},
date-added = {2011-08-29 10:29:40 -0400},
date-modified = {2011-08-29 10:32:51 -0400},
pmid = {5495015443088609266related:8g-VgG43QkwJ},
local-url = {file://localhost/Users/izaguirr/Documents/Papers/2005/Ma/Ma_2005_The%20Journal%20of%20Physical%20Chemistry%20B.pdf},
uri = {papers://7AF1B0BF-417E-4A82-A1A8-0E97759761F6/Paper/p1444},
rating = {0}
}

%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Zhao:2009p1443,
author = {R Zhao and J Shen and R.D Skeel}, 
journal = JCTC,
title = {Maximum flux transition paths of conformational change},
year = {2009},
date-added = {2011-08-29 10:02:48 -0400},
date-modified = {2011-08-29 10:03:51 -0400},
pmid = {9118122886363458929related:ca0NjHQUin4J},
local-url = {file://localhost/Users/izaguirr/Documents/Papers/2009/Zhao/Zhao_2009_Journal%20of%20chemical%20theory%20and%20computation.pdf},
uri = {papers://7AF1B0BF-417E-4A82-A1A8-0E97759761F6/Paper/p1443},
rating = {0}
}



%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Peng:2010p1442,
author = {Cheng Peng and Liqing Zhang and Teresa Head-Gordon}, 
journal = BJ,
title = {Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions},
number = {10},
pages = {2356--2364},
volume = {98},
year = {2010},
month = {May},
date-added = {2011-08-29 09:37:19 -0400},
date-modified = {2011-08-29 09:37:19 -0400},
doi = {10.1016/j.bpj.2010.01.044},
rating = {0}
}


%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{RaAr09,
author = {A Ramanathan and P.K Agarwal}, 
journal = JPCB,
title = {Computational identification of slow conformational fluctuations in proteins},
number = {52},
pages = {16669--16680},
volume = {113},
year = {2009},
date-added = {2011-06-28 01:37:34 -0400},
date-modified = {2011-06-28 01:38:31 -0400},
pmid = {14938217343728256272related:EIWALoc1T88J},
local-url = {file://localhost/Users/izaguirr/Documents/Papers/2009/Ramanathan/Ramanathan_2009_The%20Journal%20of%20Physical%20Chemistry%20B.pdf},
uri = {papers://7AF1B0BF-417E-4A82-A1A8-0E97759761F6/Paper/p560},
read = {Yes},
rating = {0}
}

%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Schuyler:2009p562,
author = {Adam D Schuyler and Robert L Jernigan and Pradman K Qasba and Boopathy Ramakrishnan and Gregory S Chirikjian}, 
journal = PSFB,
title = {Iterative cluster-{NMA}: A tool for generating conformational transitions in proteins},
number = {3},
pages = {760--776},
volume = {74},
year = {2009},
month = {Feb},
date-added = {2011-06-28 01:39:20 -0400},
date-modified = {2011-06-28 01:39:20 -0400},
doi = {10.1002/prot.22200},
read = {Yes},
rating = {0}
}

%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Skjaerven:2010p558,
author = {Lars Skjaerven and Aurora Martinez and Nathalie Reuter}, 
journal = PSFB,
title = {Principal component and normal mode analysis of proteins; a quantitative comparison using the {G}ro{EL} subunit},
number = {1},
pages = {232--243},
volume = {79},
year = {2010},
month = {Nov},
date-added = {2011-06-28 01:36:34 -0400},
date-modified = {2011-06-28 01:36:34 -0400},
doi = {10.1002/prot.22875},
read = {Yes},
rating = {0}
}

%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Singharoy:2011p1441,
author = {A Singharoy and S Cheluvaraja and P Ortoleva}, 
journal = JCP,
title = {Order parameters for macromolecules: Application to multiscale simulation},
abstract = {},
number = {4},
pages = {044104},
volume = {134},
year = {2011},
month = {Jan},
keywords = {}, 
date-added = {2011-08-28 21:27:12 -0400},
date-modified = {2011-08-28 21:27:12 -0400},
doi = {10.1063/1.35234532.2},
rating = {0}
}

%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Crooks:2011p1563,
author = {G.E Crooks and D Chandler}, 
journal = PRE,
title = {Efficient transition path sampling for nonequilibrium stochastic dynamics},
pages = {026109},
year = 2001,
volume = {64},
date-added = {2011-08-30 15:24:32 -0400},
date-modified = {2011-08-30 15:26:03 -0400},
pmid = {14570232188730263316related:FMc6sPrcM8oJ},
rating = {0}
}

@article{singhal415,
        author 	= {Nina Singhal and Christopher D. Snow and Vijay S. Pande},
        title 	= {Using path sampling to build better {M}arkovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin},
        year 	= {2004},
        journal = JCP,
        volume 	= {121},
        number 	= {1},
        pages 	= {415-425},
}

%% This BibTeX bibliography file in UTF-8 format was created using Papers.
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@article{Rogal:2008p1564,
author = {Jutta Rogal and Peter G Bolhuis}, 
journal = JCP,
title = {Multiple state transition path sampling},
abstract = {},
number = {22},
pages = {224107},
volume = {129},
year = {2008},
month = {Jan},
date-added = {2011-08-30 15:33:03 -0400},
date-modified = {2011-08-30 15:33:03 -0400},
doi = {10.1063/1.3029696},
rating = {0}
}

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@article{Bowman:2010p1565,
author = {G.R Bowman and V.A Voelz and V.S Pande}, 
journal = JACS,
title = {Atomistic Folding Simulations of the Five-Helix Bundle Protein $\lambda_{6−-85}$},
year = {2010},
date-added = {2011-08-30 15:46:27 -0400},
date-modified = {2011-08-30 15:47:23 -0400},
pmid = {2594570306520028092related:vBPnePLDASQJ},
rating = {0}
}

@article{Voelz:2010p1566,
author = {V.A Voelz and G.R Bowman and K Beauchamp and V.S Pande}, 
journal = JACS,
title = {Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder {NTL9} (1--39)},
number = {5},
pages = {1526--1528},
volume = {132},
year = {2010},
date-added = {2011-08-30 15:50:27 -0400},
date-modified = {2011-08-30 15:51:11 -0400},
pmid = {15000640445935090967related:F31RPwL7LNAJ},
rating = {0}
}

@Article{HummerMSM2008,
   Author="Buchete, N.V. and Hummer, G.",
   Title="{{C}oarse master equations for peptide folding dynamics}",
   Journal="J. Phys. Chem. B",
   Year="2008",
   Volume="112",
   Pages="6057--6069",
   Month="May"
}
@Article{ChoderaMSM2007,
   Author="Chodera, J.D. and Singhal, N. and Pande, V.S. and Dill, K.A. and Swope, W.C.",
   Title="{{A}utomatic discovery of metastable states for the construction of {M}arkov models of macromolecular conformational dynamics}",
   Journal="J. Chem. Phys.",
   Year="2007",
   Volume="126",
   Pages="155101",
   Month="Apr"
}
@Article{NoeMSMReview2008,
   Author="No\'e, F. and Fischer, S.",
   Title="{{T}ransition networks for modeling the kinetics of conformational change in macromolecules}",
   Journal="Curr. Opin. Struct. Biol.",
   Year="2008",
   Volume="18",
   Pages="154--162",
   Month="Apr"
}

%% Created using Papers on Sun, 04 Sep 2011.
%% http://mekentosj.com/papers/

@article{E:2006hg,
author = {E, Weinan and Vanden-Eijnden, Eric},
title = {{Towards a Theory of Transition Paths}},
journal = JSP,
year = {2006},
volume = {123},
number = {3},
pages = {503--523},
month = may
}

@article{Maragliano:2006kg,
author = {Maragliano, Luca and Fischer, Alexander and Vanden-Eijnden, Eric and Ciccotti, Giovanni},
title = {{String method in collective variables: Minimum free energy paths and isocommittor surfaces}},
journal = JCP,
year = {2006},
volume = {125},
number = {2},
pages = {024106}
}

@book{VandenEijnden:2006jw,
author = {Vanden-Eijnden, E},
editor = {Ferrario, Mauro and Ciccotti, Giovanni and Binder, Kurt},
title = {{Lecture Notes in Physics}},
publisher = {Springer Berlin Heidelberg},
year = {2006},
volume = {703},
series = {Lecture Notes in Physics},
address = {Berlin, Heidelberg}
}

@article{Metzner:2006du,
author = {Metzner, Philipp and Schutte, Christof and Vanden-Eijnden, Eric},
title = {{Illustration of transition path theory on a collection of simple examples}},
journal = JCP,
year = {2006},
volume = {125},
number = {8},
pages = {084110}
}

%% Created using Papers on Sun, 04 Sep 2011.
%% http://mekentosj.com/papers/

@article{Schutte:2011gs,
author = {Schutte, Christof and Noe, Frank and Lu, Jianfeng and Sarich, Marco and Vanden-Eijnden, Eric},
title = {{Markov state models based on milestoning}},
journal = JCP,
year = {2011},
volume = {134},
number = {20},
pages = {204105}
}

@article{VandenEijnden:2008bn,
author = {Vanden-Eijnden, Eric and Venturoli, Maddalena and Ciccotti, Giovanni and Elber, Ron},
title = {{On the assumptions underlying milestoning}},
journal = JCP,
year = {2008},
volume = {129},
number = {17},
pages = {174102}
}

@article{MorcosMSM2010,
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abstract = {<title>Author Summary</title> <p>Proteins in their native state can adopt a plethora of shapes, or conformations; this conformational plasticity is critical for regulation and function in many systems. However, it has remained difficult to determine what these different conformations look like at the atomic level. We present a novel way to use Nuclear Magnetic Resonance, Molecular Dynamics Simulations, and Markov State Models to uncover a map of this plethora of conformations that is consistent with the available data. We applied this method to study the intrinsic dynamics used in substrate binding by the WW domain of the Pin1 proline cis-trans isomerase and found that the NMR data were best explained by two slowly-interconverting sets of many metastable conformations rather than two distinct macrostates. Substantial value is added to the NMR data by our method since it provides a kinetic ``map'' of conformational changes consistent with the observed relaxation data. Such an approach, in combination with information theory, helped us to identify specific conformational changes that might couple substrate binding at the Pin1 WW domain to the catalytic subunit.</p>},
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pages = {e1001015},
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year = {2010},
doi = {10.1371/journal.pcbi.1001015},
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